Browsing by Author "Acharjee, A."

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Cloud Computing Enabled Big Multi-Omics Data Analytics
(SAGE Publications Inc., 2021) Koppad, S.; B, A.; Gkoutos, G.V.; Acharjee, A.
High-throughput experiments enable researchers to explore complex multifactorial diseases through large-scale analysis of omics data. Challenges for such high-dimensional data sets include storage, analyses, and sharing. Recent innovations in computational technologies and approaches, especially in cloud computing, offer a promising, low-cost, and highly flexible solution in the bioinformatics domain. Cloud computing is rapidly proving increasingly useful in molecular modeling, omics data analytics (eg, RNA sequencing, metabolomics, or proteomics data sets), and for the integration, analysis, and interpretation of phenotypic data. We review the adoption of advanced cloud-based and big data technologies for processing and analyzing omics data and provide insights into state-of-the-art cloud bioinformatics applications. © The Author(s) 2021.
Cloud Computing Enabled Big Multi-Omics Data Analytics
(SAGE Publications Inc., 2021) Koppad, S.; B, A.; Gkoutos, G.V.; Acharjee, A.
High-throughput experiments enable researchers to explore complex multifactorial diseases through large-scale analysis of omics data. Challenges for such high-dimensional data sets include storage, analyses, and sharing. Recent innovations in computational technologies and approaches, especially in cloud computing, offer a promising, low-cost, and highly flexible solution in the bioinformatics domain. Cloud computing is rapidly proving increasingly useful in molecular modeling, omics data analytics (eg, RNA sequencing, metabolomics, or proteomics data sets), and for the integration, analysis, and interpretation of phenotypic data. We review the adoption of advanced cloud-based and big data technologies for processing and analyzing omics data and provide insights into state-of-the-art cloud bioinformatics applications. Â© The Author(s) 2021.
Machine Learning-Based Identification of Colon Cancer Candidate Diagnostics Genes
(MDPI, 2022) Koppad, S.; Annappa, A.; Nash, K.; Gkoutos, G.V.; Acharjee, A.
Background: Colorectal cancer (CRC) is the third leading cause of cancer-related death and the fourth most commonly diagnosed cancer worldwide. Due to a lack of diagnostic biomarkers and understanding of the underlying molecular mechanisms, CRC’s mortality rate continues to grow. CRC occurrence and progression are dynamic processes. The expression levels of specific molecules vary at various stages of CRC, rendering its early detection and diagnosis challenging and the need for identifying accurate and meaningful CRC biomarkers more pressing. The advances in high-throughput sequencing technologies have been used to explore novel gene expression, targeted treatments, and colon cancer pathogenesis. Such approaches are routinely being applied and result in large datasets whose analysis is increasingly becoming dependent on machine learning (ML) algorithms that have been demonstrated to be computationally efficient platforms for the identification of variables across such high-dimensional datasets. Methods: We developed a novel ML-based experimental design to study CRC gene associations. Six different machine learning methods were employed as classifiers to identify genes that can be used as diagnostics for CRC using gene expression and clinical datasets. The accuracy, sensitivity, specificity, F1 score, and area under receiver operating characteristic (AUROC) curve were derived to explore the differentially expressed genes (DEGs) for CRC diagnosis. Gene ontology enrichment analyses of these DEGs were performed and predicted gene signatures were linked with miRNAs. Results: We evaluated six machine learning classification methods (Adaboost, ExtraTrees, logistic regression, naïve Bayes classifier, random forest, and XGBoost) across different combinations of training and test datasets over GEO datasets. The accuracy and the AUROC of each combination of training and test data with different algorithms were used as comparison metrics. Random forest (RF) models consistently performed better than other models. In total, 34 genes were identified and used for pathway and gene set enrichment analysis. Further mapping of the 34 genes with miRNA identified interesting miRNA hubs genes. Conclusions: We identified 34 genes with high accuracy that can be used as a diagnostics panel for CRC. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.
Transfer Learning Based Model for Colon Cancer Prediction Using VGG16
(Institute of Electrical and Electronics Engineers Inc., 2023) Koppad, S.; Annappa, B.; Acharjee, A.
Colon cancer, or a colorectal cancer, is a malignant neoplasm that originates in the colon. It is one of the most prevalent forms of cancer globally, with significant impacts on morbidity and mortality rates. The essential task is to detect it and detect it at an initial phase for curing the patient precisely. The artificial intelligence plays important roles in the colon cancer prediction. The authors proposed various models on colon cancer prediction using ML and DL. The existing approaches are unable to achieve good accuracy for the colon cancer prediction. This research work suggests a transfer learning based framework for the colon cancer prediction. This framework is planned on the basis of VGG16 and CNN in colon cancer prediction. The proposed framework is implemented in python and results is analysed concerning accuracy, precision, recall. Â© 2023 IEEE.